repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
value |
|---|---|---|---|---|---|---|
Multi2WOZ | Multi2WOZ-main/downstream/utils/utils_domain.py | import torch
import torch.utils.data as data
import random
import math
from .dataloader_dst import *
from .dataloader_nlg import *
from .dataloader_nlu import *
from .dataloader_dm import *
from .dataloader_usdl import *
def get_loader(args, mode, tokenizer, datasets, unified_meta, shuffle=False):
task = args["ta... | 3,348 | 39.349398 | 122 | py |
Multi2WOZ | Multi2WOZ-main/downstream/utils/utils_camrest676.py | import json
import ast
import collections
import os
from .utils_function import get_input_example
def read_langs_turn(args, file_name, max_line = None):
print(("Reading from {} for read_langs_turn".format(file_name)))
data = []
with open(file_name) as f:
dials = json.load(f)
... | 2,180 | 28.472973 | 93 | py |
Multi2WOZ | Multi2WOZ-main/downstream/utils/utils_universal_act.py | import json
import ast
import os
from .utils_function import get_input_example
def read_langs_turn(file_name, max_line = None):
print(("Reading from {} for read_langs_turn".format(file_name)))
data = []
domain_counter = {}
with open(file_name) as f:
dials = json.load(f)
... | 4,855 | 43.550459 | 103 | py |
Multi2WOZ | Multi2WOZ-main/downstream/utils/multiwoz/nlp.py | import math
import re
from collections import Counter
from nltk.util import ngrams
timepat = re.compile("\d{1,2}[:]\d{1,2}")
pricepat = re.compile("\d{1,3}[.]\d{1,2}")
fin = open('utils/multiwoz/mapping.pair', 'r')
replacements = []
for line in fin.readlines():
tok_from, tok_to = line.replace('\n', '').split('\... | 7,781 | 30.763265 | 124 | py |
Multi2WOZ | Multi2WOZ-main/downstream/utils/multiwoz/delexicalize.py | import re
import simplejson as json
from .nlp import normalize
digitpat = re.compile('\d+')
timepat = re.compile("\d{1,2}[:]\d{1,2}")
pricepat2 = re.compile("\d{1,3}[.]\d{1,2}")
# FORMAT
# domain_value
# restaurant_postcode
# restaurant_address
# taxi_car8
# taxi_number
# train_id etc..
def prepareSlotValuesIndep... | 6,421 | 42.391892 | 100 | py |
Multi2WOZ | Multi2WOZ-main/downstream/utils/multiwoz/dbPointer.py |
import sqlite3
import numpy as np
from .nlp import normalize
# loading databases
domains = ['restaurant', 'hotel', 'attraction', 'train', 'taxi', 'hospital']#, 'police']
dbs = {}
for domain in domains:
db = 'data/multi-woz/db/{}-dbase.db'.format(domain)
conn = sqlite3.connect(db)
c = conn.cursor()
... | 6,600 | 37.377907 | 137 | py |
Multi2WOZ | Multi2WOZ-main/downstream/utils/multiwoz/fix_label.py |
def fix_general_label_error(labels, type, slots, ontology_version=""):
label_dict = dict([ (l[0], l[1]) for l in labels]) if type else dict([ (l["slots"][0][0], l["slots"][0][1]) for l in labels])
GENERAL_TYPO = {
# type
"guesthouse":"guest house","guesthouses":"guest house","guest":"guest ho... | 24,598 | 59.439803 | 167 | py |
Multi2WOZ | Multi2WOZ-main/downstream/utils/metrics/measures.py | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy
import os
import re
import subprocess
import tempfile
import numpy as np
from six.moves import urllib
def word_error_rate(r, h):
"""
This is a func... | 4,190 | 35.12931 | 99 | py |
Multi2WOZ | Multi2WOZ-main/downstream/utils/loss_function/masked_cross_entropy.py | import torch
from torch.nn import functional
from torch.autograd import Variable
from utils.config import *
import torch.nn as nn
import numpy as np
def sequence_mask(sequence_length, max_len=None):
if max_len is None:
max_len = sequence_length.data.max()
batch_size = sequence_length.size(0)
seq_ra... | 6,501 | 36.802326 | 92 | py |
custom-diffusion | custom-diffusion-main/sample.py | # This code is built from the Stable Diffusion repository: https://github.com/CompVis/stable-diffusion.
# Copyright (c) 2022 Robin Rombach and Patrick Esser and contributors.
# CreativeML Open RAIL-M
#
# ==========================================================================================
#
# Adobe’s modifications... | 27,272 | 62.131944 | 1,097 | py |
custom-diffusion | custom-diffusion-main/train.py | # This code is built from the Stable Diffusion repository: https://github.com/CompVis/stable-diffusion.
# Copyright (c) 2022 Robin Rombach and Patrick Esser and contributors.
# CreativeML Open RAIL-M
#
# ==========================================================================================
#
# Adobe’s modifications... | 48,845 | 48.389282 | 1,097 | py |
custom-diffusion | custom-diffusion-main/src/diffusers_model_pipeline.py | # This code is built from the Huggingface repository: https://github.com/huggingface/diffusers/blob/main/examples/dreambooth/train_dreambooth.py, and
# https://github.com/huggingface/diffusers/blob/main/examples/textual_inversion/textual_inversion.py
# Copyright 2022- The Hugging Face team. All rights reserved.
# ... | 25,547 | 50.198397 | 149 | py |
custom-diffusion | custom-diffusion-main/src/diffusers_training.py | # This code is built from the Huggingface repository: https://github.com/huggingface/diffusers/blob/main/examples/dreambooth/train_dreambooth.py, and
# https://github.com/huggingface/diffusers/blob/main/examples/textual_inversion/textual_inversion.py
# Copyright 2022- The Hugging Face team. All rights reserved.
# ... | 51,778 | 45.816456 | 253 | py |
custom-diffusion | custom-diffusion-main/src/compress.py | # Copyright 2022 Adobe Research. All rights reserved.
# To view a copy of the license, visit LICENSE.md.
import torch
import argparse
def compress(delta_ckpt, ckpt, diffuser=False, compression_ratio=0.6, device='cuda'):
st = torch.load(f'{delta_ckpt}')
if not diffuser:
compressed_key = 'state_dict'
... | 2,479 | 34.428571 | 107 | py |
custom-diffusion | custom-diffusion-main/src/diffusers_data_pipeline.py | # This code is built from the Huggingface repository: https://github.com/huggingface/diffusers/blob/main/examples/dreambooth/train_dreambooth.py, and
# https://github.com/huggingface/diffusers/blob/main/examples/textual_inversion/textual_inversion.py
# Copyright 2022- The Hugging Face team. All rights reserved.
# ... | 20,730 | 50.061576 | 161 | py |
custom-diffusion | custom-diffusion-main/src/diffusers_composenW.py | # Copyright 2022 Adobe Research. All rights reserved.
# To view a copy of the license, visit LICENSE.md.
import sys
import os
import argparse
import torch
from scipy.linalg import lu_factor, lu_solve
sys.path.append('./')
from diffusers import StableDiffusionPipeline
from src import diffusers_sample
def gdupdateWe... | 7,508 | 37.706186 | 172 | py |
custom-diffusion | custom-diffusion-main/src/model.py | # This code is built from the Stable Diffusion repository: https://github.com/CompVis/stable-diffusion.
# Copyright (c) 2022 Robin Rombach and Patrick Esser and contributors.
# CreativeML Open RAIL-M
#
# ==========================================================================================
#
# Adobe’s modifications... | 29,720 | 70.102871 | 1,097 | py |
custom-diffusion | custom-diffusion-main/src/custom_modules.py | # This code is built from the Huggingface repository: https://github.com/huggingface/transformers/tree/main/src/transformers/models/clip.
# Copyright 2018- The Hugging Face team. All rights reserved.
# Apache License
# Version 2.0, January 2004
# ... | 16,723 | 50.937888 | 137 | py |
custom-diffusion | custom-diffusion-main/src/finetune_data.py | # This code is built from the Stable Diffusion repository: https://github.com/CompVis/stable-diffusion.
# Copyright (c) 2022 Robin Rombach and Patrick Esser and contributors.
# CreativeML Open RAIL-M
#
# ==========================================================================================
#
# Adobe’s modifications... | 22,159 | 81.686567 | 1,097 | py |
custom-diffusion | custom-diffusion-main/src/retrieve.py | # Copyright 2022 Adobe Research. All rights reserved.
# To view a copy of the license, visit LICENSE.md.
import argparse
import os
import tqdm
from pathlib import Path
import requests
from PIL import Image
from io import BytesIO
from clip_retrieval.clip_client import ClipClient
def retrieve(target_name, outpath, num... | 2,989 | 31.150538 | 143 | py |
custom-diffusion | custom-diffusion-main/src/get_deltas.py | # Copyright 2022 Adobe Research. All rights reserved.
# To view a copy of the license, visit LICENSE.md.
import os
import argparse
import glob
import torch
def main(path, newtoken=0):
layers = []
for files in glob.glob(f'{path}/checkpoints/*'):
if ('=' in files or '_' in files) and 'delta' not in file... | 2,047 | 36.925926 | 149 | py |
custom-diffusion | custom-diffusion-main/src/composenW.py | # Copyright 2022 Adobe Research. All rights reserved.
# To view a copy of the license, visit LICENSE.md.
import sys
import os
import argparse
import random
import torch
import torchvision
import numpy as np
from tqdm import tqdm
from scipy.linalg import lu_factor, lu_solve
sys.path.append('stable-diffusion')
sys.pa... | 11,722 | 38.738983 | 130 | py |
custom-diffusion | custom-diffusion-main/src/convert.py | # Copyright 2022 Adobe Research. All rights reserved.
# To view a copy of the license, visit LICENSE.md.
import os, sys
import argparse
import torch
from omegaconf import OmegaConf
from ldm.util import instantiate_from_config
sys.path.append('stable-diffusion')
sys.path.append('./')
from src.diffusers_model_pipeline i... | 7,914 | 47.858025 | 161 | py |
custom-diffusion | custom-diffusion-main/src/__init__.py | 0 | 0 | 0 | py | |
custom-diffusion | custom-diffusion-main/src/diffusers_sample.py | # ==========================================================================================
#
# MIT License. To view a copy of the license, visit MIT_LICENSE.md.
#
# ==========================================================================================
import argparse
import sys
import os
import numpy as np
impor... | 3,037 | 39.506667 | 122 | py |
custom-diffusion | custom-diffusion-main/customconcept101/evaluate.py | import argparse
import glob
import json
import os
import warnings
from pathlib import Path
import clip
import numpy as np
import pandas as pd
import sklearn.preprocessing
import torch
from packaging import version
from PIL import Image
from torchvision.transforms import CenterCrop, Compose, Normalize, Resize, ToTensor... | 10,450 | 33.953177 | 122 | py |
BioSimulator.jl | BioSimulator.jl-master/benchmarks/stochpy_bench.py | import stochpy
import statistics as stats
from statsmodels import robust
import argparse
import random
import sys
def benchmark(fdir, method, tfinal, nsaves, nreal, seed, n_sample):
# initialize
smod = stochpy.SSA()
times = []
smod.Model(model_file='stochpy.psc', dir=fdir)
random.seed(seed)
for i in ran... | 1,358 | 22.033898 | 79 | py |
globus-automate-client | globus-automate-client-main/examples/sdk_scripts/flow_deploy_and_run.py | #!/usr/bin/env python
import json
import sys
from globus_automate_client import create_flows_client
def main():
flow_file = sys.argv[1]
with open(flow_file, "r") as ff:
flow_dict = json.load(ff)
flow_input = sys.argv[2]
with open(flow_input, "r") as fi:
flow_input_data = json.load(fi)... | 773 | 24.8 | 70 | py |
globus-automate-client | globus-automate-client-main/tests/conftest.py | import pytest
import responses
@pytest.fixture(autouse=True)
def mocked_responses():
"""Mock responses to requests."""
with responses.RequestsMock() as request_mock:
yield request_mock
| 204 | 17.636364 | 50 | py |
globus-automate-client | globus-automate-client-main/tests/test_flows_client.py | import json
import os
import pathlib
import urllib.parse
from typing import Any, Dict, Union, cast
from unittest.mock import Mock
import pytest
import yaml
from globus_automate_client import flows_client
VALID_FLOW_DEFINITION = {
"StartAt": "perfect",
"States": {
"perfect": {
"Type": "Pas... | 36,535 | 35.609218 | 87 | py |
globus-automate-client | globus-automate-client-main/tests/test_init.py | import inspect
import globus_automate_client
def test_all_exports():
"""Validate that all imported names are listed in __all__."""
imported = set(
name
for name in dir(globus_automate_client)
if (
not name.startswith("__")
and not inspect.ismodule(getattr(glob... | 490 | 24.842105 | 75 | py |
globus-automate-client | globus-automate-client-main/tests/test_sdk_v3.py | from typing import Iterable
import pytest
import globus_automate_client
from globus_automate_client.cli.constants import (
ActionRole,
ActionRoleAllNames,
ActionRoleDeprecated,
FlowRole,
FlowRoleAllNames,
FlowRoleDeprecated,
)
def test_import():
assert bool(globus_automate_client)
@pyt... | 898 | 22.051282 | 64 | py |
globus-automate-client | globus-automate-client-main/tests/test_action_client.py | import json
import urllib.parse
import uuid
import pytest
import responses
from globus_automate_client import action_client
@pytest.fixture
def ac():
yield action_client.ActionClient()
@pytest.mark.parametrize(
"data, expected",
(
({"globus_auth_scope": "success"}, "success"),
({}, "")... | 5,532 | 33.798742 | 86 | py |
globus-automate-client | globus-automate-client-main/tests/test_helpers.py | import pytest
from globus_automate_client import helpers
@pytest.mark.parametrize(
"args, expected, message",
(
# Null
((None, {}), None, "If nothing is specified, None must be returned"),
#
# List with no dict keys
(([], {}), set(), "empty list identity not maintained... | 4,584 | 35.102362 | 88 | py |
globus-automate-client | globus-automate-client-main/docs/source/conf.py | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... | 1,983 | 28.61194 | 79 | py |
globus-automate-client | globus-automate-client-main/docs/source/code_snippets/premade_authorizers.py | import os
from globus_sdk import AccessTokenAuthorizer
from globus_automate_client import FlowsClient
from globus_automate_client.cli.auth import CLIENT_ID
from globus_automate_client.flows_client import AllowedAuthorizersType
def authorizer_retriever(
flow_url: str, flow_scope: str, client_id: str
) -> Allowed... | 2,037 | 34.137931 | 78 | py |
globus-automate-client | globus-automate-client-main/docs/source/code_snippets/runner.py | import logging
import os
import pathlib
import queue
import sys
# The flow to run.
FLOW_ID = "your-flow-id-here"
# The flow will be run X seconds after the most recent filesystem event is received.
# If no filesystem events are ever received, the flow will not be run.
COOL_OFF_TIME_S = 60
logging.basicConfig(
l... | 3,029 | 27.857143 | 88 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/graphviz_rendering.py | import json
from typing import Any, Dict, List, Mapping, Optional
from graphviz import Digraph
_SHAPE_TYPES = {
"Choice": {"shape": "diamond"},
"Action": {"shape": "box"},
"Succeed": {"shape": "box", "style": "rounded"},
}
_COLOR_PRECEDENCE = ["", "yellow", "orange", "green", "red"]
def json_to_label_t... | 3,145 | 36.903614 | 86 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/client_helpers.py | import typing as t
from globus_sdk.authorizers import GlobusAuthorizer
from globus_automate_client.action_client import ActionClient
from globus_automate_client.cli.auth import CLIENT_ID, get_cli_authorizer
from globus_automate_client.flows_client import (
MANAGE_FLOWS_SCOPE,
PROD_FLOWS_BASE_URL,
FlowsCli... | 5,518 | 40.810606 | 91 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/__init__.py | from .action_client import ActionClient
from .cli.auth import get_authorizer_for_scope
from .client_helpers import create_action_client, create_flows_client
from .flows_client import FlowsClient, validate_flow_definition
from .graphviz_rendering import graphviz_format, state_colors_for_log
from .queues_client import Qu... | 625 | 30.3 | 69 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/action_client.py | import os
import uuid
from typing import Any, Dict, Iterable, List, Mapping, Optional, Type, TypeVar, Union
from urllib.parse import quote, urlparse
from globus_sdk import BaseClient, GlobusHTTPResponse
from globus_sdk.authorizers import GlobusAuthorizer
from .helpers import merge_keywords
_ActionClient = TypeVar("_... | 9,799 | 37.582677 | 91 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/flows_client.py | import contextlib
import json
import os
import warnings
from pathlib import Path
from typing import (
Any,
Callable,
Dict,
Iterable,
List,
Mapping,
Optional,
Sequence,
Set,
Tuple,
Type,
TypeVar,
Union,
)
from urllib.parse import quote, urljoin, urlparse
from globus_s... | 51,219 | 37.80303 | 88 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/helpers.py | from typing import Any, Dict, Iterable, List, Optional, Set, Tuple, Union
def merge_keywords(
base: Optional[Iterable[str]],
kwargs: Dict[str, Union[str, Iterable[str]]],
*keywords: str,
) -> Optional[List[str]]:
"""Merge all given keyword parameter aliases and deduplicate the values.
.. warning... | 3,903 | 32.655172 | 88 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/queues_client.py | import uuid
from typing import Any, Dict, List, Optional
from globus_sdk import (
AccessTokenAuthorizer,
BaseClient,
ClientCredentialsAuthorizer,
GlobusHTTPResponse,
RefreshTokenAuthorizer,
)
from globus_automate_client.cli.auth import get_authorizer_for_scope
_prod_queues_base_url = "https://que... | 5,346 | 32.41875 | 88 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/cli/auth.py | import copy
import json
import os
import pathlib
import platform
import sys
from json import JSONDecodeError
from typing import Any, Callable, Dict, List, NamedTuple, Optional, Set, Union, cast
import click
import typer
from globus_sdk import (
AuthAPIError,
AuthClient,
GlobusAPIError,
NativeAppAuthCli... | 14,482 | 33.898795 | 87 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/cli/main.py | try:
from importlib.metadata import version as get_version # type: ignore
except ImportError:
# Python < 3.8
from importlib_metadata import version as get_version
import typer
import yaml
from globus_automate_client.cli import actions, flows, queues, session
from globus_automate_client.cli.auth import DE... | 1,330 | 22.350877 | 78 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/cli/callbacks.py | import json
import os
import pathlib
import re
from errno import ENAMETOOLONG
from typing import AbstractSet, Callable, List, Optional, cast
from urllib.parse import urlparse
import typer
import yaml
from globus_sdk import AuthClient
from .auth import get_authorizer_for_scope
_uuid_regex = (
"([a-fA-F0-9]{8}-[a-... | 5,537 | 32.161677 | 83 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/cli/rich_rendering.py | from rich.console import Group
from rich.live import Live
class Content:
"""
This class represents a per CLI invocation "canvas" which will hold the data
that gets displayed on the CLI. All content updates happen by updating the
value of the instance's RenderGroup
"""
rg: Group = Group()
... | 455 | 21.8 | 80 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/cli/constants.py | import enum
import typer
from globus_sdk import GlobusHTTPResponse
from globus_automate_client.graphviz_rendering import (
graphviz_format,
state_colors_for_log,
)
class FlowRole(str, enum.Enum):
flow_viewer = "flow_viewer"
flow_starter = "flow_starter"
flow_administrator = "flow_administrator"
... | 4,445 | 26.614907 | 88 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/cli/rich_helpers.py | import abc
import collections
import functools
import json
from time import sleep
from typing import Any, Callable, Dict, List, Optional, Set, Type, Union, cast
import arrow
import typer
import yaml
from globus_sdk import AuthClient, BaseClient, GlobusAPIError, GlobusHTTPResponse
from requests import Response
from ric... | 13,647 | 29.600897 | 86 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/cli/actions.py | import functools
from typing import List
import typer
from globus_automate_client.cli.callbacks import (
input_validator,
principal_validator,
url_validator_callback,
)
from globus_automate_client.cli.constants import OutputFormat
from globus_automate_client.cli.helpers import (
output_format_option,
... | 9,011 | 29.969072 | 88 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/cli/session.py | import json
import typer
from globus_automate_client.cli.auth import get_current_user, logout, revoke_login
from globus_automate_client.cli.helpers import verbosity_option
app = typer.Typer(short_help="Manage your session with the Automate Command Line")
@app.command("whoami")
def session_whoami(verbose: bool = ve... | 1,256 | 27.568182 | 82 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/cli/queues.py | import functools
from enum import Enum
from typing import List
import typer
from globus_automate_client.cli.auth import CLIENT_ID
from globus_automate_client.cli.callbacks import input_validator, principal_validator
from globus_automate_client.cli.constants import OutputFormat
from globus_automate_client.cli.helpers ... | 8,256 | 30.880309 | 88 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/cli/helpers.py | import json
from typing import Any, Callable, Dict, List, Mapping, Optional, Union
import requests
import typer
import yaml
from globus_sdk import GlobusAPIError, GlobusHTTPResponse
from globus_automate_client.cli.callbacks import flows_endpoint_envvar_callback
from globus_automate_client.cli.constants import (
A... | 3,446 | 28.715517 | 86 | py |
globus-automate-client | globus-automate-client-main/globus_automate_client/cli/flows.py | import functools
import textwrap
import uuid
import warnings
from typing import Any, List, Optional, Tuple
import typer
from globus_automate_client.cli.auth import CLIENT_ID
from globus_automate_client.cli.callbacks import (
custom_principal_validator,
flow_input_validator,
input_validator,
principal_... | 50,154 | 32.237243 | 88 | py |
simanneal | simanneal-master/setup.py | #!/usr/bin/env/python
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
LONG_DESCRIPTION = """`simanneal` is a python implementation of the
[simulated annealing optimization](http://en.wikipedia.org/wiki/Simulated_annealing) technique.
Simulated annealing is used to find a... | 1,231 | 33.222222 | 96 | py |
simanneal | simanneal-master/examples/salesman.py | # -*- coding: utf-8 -*-
from __future__ import print_function
import math
import random
from collections import defaultdict
from simanneal import Annealer
def distance(a, b):
"""Calculates distance between two latitude-longitude coordinates."""
R = 3963 # radius of Earth (miles)
lat1, lon1 = math.radians... | 3,152 | 31.84375 | 81 | py |
simanneal | simanneal-master/examples/watershed/shapefile.py | """
shapefile.py
Provides read and write support for ESRI Shapefiles.
author: jlawhead<at>geospatialpython.com
date: 20110927
version: 1.1.4
Compatible with Python versions 2.4-3.x
"""
from struct import pack, unpack, calcsize, error
import os
import sys
import time
import array
#
# Constants for shape types
NULL = 0
... | 38,106 | 36.993021 | 136 | py |
simanneal | simanneal-master/examples/watershed/watershed_condition.py | import math
import sys
import os
sys.path.append(os.path.abspath('../'))
from anneal import Annealer
import shapefile
import random
#-----------------------------------------------#
#-------------- Configuration ------------------#
#-----------------------------------------------#
shp = './data/huc6_4326.shp'
specie... | 5,505 | 27.677083 | 105 | py |
simanneal | simanneal-master/tests/test_anneal.py | import random
import sys
import time
from helper import distance, cities, distance_matrix
from simanneal import Annealer
if sys.version_info.major >= 3: # pragma: no cover
from io import StringIO
else:
from StringIO import StringIO
class TravellingSalesmanProblem(Annealer):
"""Test annealer with a trav... | 4,323 | 32.007634 | 98 | py |
simanneal | simanneal-master/tests/helper.py | import math
def distance(a, b):
"""Calculates distance between two latitude-longitude coordinates."""
R = 3963 # radius of Earth (miles)
lat1, lon1 = math.radians(a[0]), math.radians(a[1])
lat2, lon2 = math.radians(b[0]), math.radians(b[1])
return math.acos(math.sin(lat1) * math.sin(lat2) +
... | 1,354 | 29.111111 | 81 | py |
simanneal | simanneal-master/simanneal/__init__.py | from __future__ import absolute_import
from .anneal import Annealer
__all__ = ['Annealer']
__version__ = "0.5.0"
| 114 | 18.166667 | 38 | py |
simanneal | simanneal-master/simanneal/anneal.py | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import abc
import copy
import datetime
import math
import pickle
import random
import signal
import sys
import time
def round_figures(x, n):
"""Returns x rounded to ... | 11,213 | 34.6 | 111 | py |
EASIER | EASIER-master/easier-dataAnalyst/src/myfunction.py | #myfunction.py
import numpy as np
from math import pow, sqrt
from operator import itemgetter
def norm2perfq(min_perfq, max_perfq, value, min, max):
return min_perfq + (max_perfq - min_perfq) * (value - min) / (max - min)
def getpoint(data, index):
try:
return data[np.where(data[:, 0] == index)[0][0... | 1,787 | 30.928571 | 101 | py |
EASIER | EASIER-master/easier-dataAnalyst/src/easier-lengths.py | # 0 - solution number,
# 1 - PA,
# 2 - PerfQ,
# 3 - Dist
import numpy as np
import myfunction
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
base_dir = '../data/'
# Near-Pareto frontier from a chromosome long 4
pareto_folder_l4 = base_dir + 'FTA/length_4/pareto/'
file_l4 = pareto_fol... | 4,969 | 38.444444 | 122 | py |
EASIER | EASIER-master/easier-dataAnalyst/src/easier_population.py | #easier_long
import numpy as np
import myfunction
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
base_dir = '../data/'
# Near-Pareto frontier
pareto_folder_64_E1280 = base_dir + 'FTA/64/lenght_4/pareto/P_64_E_1280_X_0.8_M_0.2__18.10.03.11.03.58__/'
file_64_E1280 = pareto_folder_64_E1280 + 'P... | 4,750 | 42.990741 | 141 | py |
EASIER | EASIER-master/easier-dataAnalyst/src/easier_long.py | #easier_long
import numpy as np
import myfunction
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
base_dir = '../data/'
# Near-Pareto frontier from a chromosome long 4
pareto_folder_64_l4 = base_dir + 'FTA/64/lenght_4/pareto/P_64_E_1280_X_0.8_M_0.2__18.10.03.11.03.58__/'
file_64_l4 = pareto_f... | 3,488 | 37.340659 | 123 | py |
EASIER | EASIER-master/easier-dataAnalyst/src/easier_evolution.py | #easier_long
import numpy as np
import myfunction
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
base_dir = '../data/'
# Near-Pareto frontier from a chromosome long 4
pareto_folder_64_E1280 = base_dir + 'FTA/64/lenght_4/pareto/P_64_E_1280_X_0.8_M_0.2__18.10.03.11.03.58__/'
file_64_E1280 = pa... | 4,659 | 41.363636 | 141 | py |
AnalyzeParameterEfficientFinetune | AnalyzeParameterEfficientFinetune-main/src/zlog.py | import os
import time
import torch
import traceback
from contextlib import contextmanager
from tensorboardX import SummaryWriter # maple
import jiant.utils.python.io as py_io
import jiant.utils.python.filesystem as filesystem
class BaseZLogger:
def log_context(self):
raise NotImplementedError()
def... | 7,042 | 27.864754 | 112 | py |
AnalyzeParameterEfficientFinetune | AnalyzeParameterEfficientFinetune-main/src/runscript.py | import os
import torch
from transformers import AutoConfig
import jiant.proj.main.write_task_configs as write_task_configs
import jiant.proj.main.export_model as export_model
#import jiant.proj.main.tokenize_and_cache as tokenize_and_cache
import tokenize_and_cache # maple
import jiant.proj.main.scripts.configurator... | 13,469 | 43.163934 | 201 | py |
AnalyzeParameterEfficientFinetune | AnalyzeParameterEfficientFinetune-main/src/evaluate.py | import json
import os
import torch
import jiant.utils.python.io as py_io
import jiant.proj.main.components.task_sampler as jiant_task_sampler
from jiant.proj.main.components.evaluate import *
def write_val_results(val_results_dict, metrics_aggregator, output_dir, verbose=True, result_file = "val_metrics.json"):
... | 1,180 | 38.366667 | 120 | py |
AnalyzeParameterEfficientFinetune | AnalyzeParameterEfficientFinetune-main/src/metarunner.py | import jiant.proj.main.metarunner as jiant_metarunner
from jiant.utils.zlog import BaseZLogger, PRINT_LOGGER
import jiant.proj.main.runner as jiant_runner
class JiantMetarunner(jiant_metarunner.JiantMetarunner):
def __init__(
self,
runner: jiant_runner.JiantRunner,
save_every_steps,
... | 1,294 | 32.205128 | 134 | py |
AnalyzeParameterEfficientFinetune | AnalyzeParameterEfficientFinetune-main/src/container_setup.py | import warnings
from dataclasses import dataclass
from typing import Dict, List, Optional
import jiant.proj.main.components.task_sampler as jiant_task_sampler
import jiant.shared.caching as caching
from jiant.tasks.core import Task
from jiant.tasks.retrieval import create_task_from_config_path
import jiant.utils.pytho... | 5,589 | 47.189655 | 100 | py |
AnalyzeParameterEfficientFinetune | AnalyzeParameterEfficientFinetune-main/src/runner.py | from http.client import NotConnected
from typing import Dict
from dataclasses import dataclass
import torch
import math
import numpy as np
import copy
#from functorch import *
from torch.autograd.functional import *
import jiant.tasks.evaluate as evaluate
import jiant.utils.torch_utils as torch_utils
#from jiant.pro... | 45,479 | 47.177966 | 202 | py |
AnalyzeParameterEfficientFinetune | AnalyzeParameterEfficientFinetune-main/src/model_setup.py | import transformers
import torch
from jiant.ext.radam import RAdam
class OptimizerScheduler:
def __init__(self, optimizer, scheduler):
super().__init__()
self.optimizer = optimizer
self.scheduler = scheduler
def step(self):
self.optimizer.step()
self.scheduler.step()
... | 6,050 | 30.515625 | 112 | py |
AnalyzeParameterEfficientFinetune | AnalyzeParameterEfficientFinetune-main/src/main_runscript.py | import os
import torch
import datetime
import jiant.proj.main.modeling.model_setup as jiant_model_setup
import runner as jiant_runner
#import jiant.proj.main.components.container_setup as container_setup
#import jiant.proj.main.metarunner as jiant_metarunner
import metarunner as jiant_metarunner
#import jiant.proj.ma... | 15,719 | 41.95082 | 200 | py |
AnalyzeParameterEfficientFinetune | AnalyzeParameterEfficientFinetune-main/src/tokenize_and_cache.py | import os
from transformers import AutoConfig
from transformers import AutoTokenizer
import jiant.proj.main.preprocessing as preprocessing
import jiant.shared.caching as shared_caching
import jiant.tasks.evaluate as evaluate
import jiant.utils.python.io as py_io
import jiant.utils.zconf as zconf
from jiant.proj.main... | 4,884 | 36.290076 | 100 | py |
pdbfixer | pdbfixer-master/setup.py | """pdbfixer: Fixes problems in PDB files
Protein Data Bank (PDB) files often have a number of problems that must be
fixed before they can be used in a molecular dynamics simulation. The details
vary depending on how the file was generated. Here are some of the most common
ones:
- If the structure was generated by X-r... | 3,004 | 36.5625 | 81 | py |
pdbfixer | pdbfixer-master/devtools/createSoftForcefield.py | """
createSoftForceField.py: Creates a force field XML file that is suitable
for removing clashes in very badly strained systems.
This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the... | 6,801 | 40.987654 | 145 | py |
pdbfixer | pdbfixer-master/devtools/travis-ci/push-docs-to-s3.py | #!/usr/bin/env python
"""
Must have the vollowing environment variables defined:
* BUCKET_NAME : AWS bucket name
* PREFIX : 'latest' or other version number
"""
import os
import pip
import tempfile
import subprocess
import thermopyl.version
BUCKET_NAME = 'thermopyl.org'
if not thermopyl.version.release:
PREFIX... | 1,410 | 27.795918 | 81 | py |
pdbfixer | pdbfixer-master/pdbfixer/ui.py | from __future__ import absolute_import
import webbrowser
import os.path
import time
import sys
from math import sqrt
import openmm.app as app
import openmm.unit as unit
from openmm.vec3 import Vec3
from .pdbfixer import PDBFixer, proteinResidues, dnaResidues, rnaResidues, _guessFileFormat
from . import uiserver
if ... | 12,126 | 41.85159 | 223 | py |
pdbfixer | pdbfixer-master/pdbfixer/uiserver.py | from threading import Thread
import cgi
import sys
try:
from socketserver import ThreadingMixIn
from http.server import HTTPServer, BaseHTTPRequestHandler
from urllib.parse import parse_qs
except:
from SocketServer import ThreadingMixIn
from BaseHTTPServer import HTTPServer, BaseHTTPRequestHandler
... | 2,717 | 31.746988 | 154 | py |
pdbfixer | pdbfixer-master/pdbfixer/pdbfixer.py | """
pdbfixer.py: Fixes problems in PDB files
This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.
Portio... | 60,255 | 45.350769 | 228 | py |
pdbfixer | pdbfixer-master/pdbfixer/__init__.py | from __future__ import absolute_import
from .pdbfixer import PDBFixer
| 71 | 17 | 38 | py |
pdbfixer | pdbfixer-master/pdbfixer/tests/test_mutate.py | import openmm.app as app
import pdbfixer
import tempfile
from pytest import raises
def test_mutate_1():
fixer = pdbfixer.PDBFixer(pdbid='1VII')
fixer.applyMutations(["ALA-57-GLY"], "A")
fixer.findMissingResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.addMissingHyd... | 2,999 | 41.253521 | 156 | py |
pdbfixer | pdbfixer-master/pdbfixer/tests/test_cli.py | #!/usr/bin/python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Test command-line interface.
"""
#===================================================... | 1,855 | 31.561404 | 118 | py |
pdbfixer | pdbfixer-master/pdbfixer/tests/test_build_and_simulate.py |
from __future__ import print_function
import pdbfixer
import openmm
import os
import os.path
import sys
import numpy
import tempfile
from threading import Timer
#from a solution on stackoverflow
class Watchdog(BaseException):
def __init__(self, timeout, userHandler=None): # timeout in seconds
self.time... | 9,799 | 45.445498 | 2,624 | py |
pdbfixer | pdbfixer-master/pdbfixer/tests/__init__.py | 0 | 0 | 0 | py | |
pdbfixer | pdbfixer-master/pdbfixer/tests/test_removechains.py | import openmm.app as app
import pdbfixer
import tempfile
import time
from pathlib import Path
from urllib.request import urlopen
from io import StringIO
import pytest
@pytest.fixture(scope="module")
def file_content():
return (Path(__file__).parent / "data" / "4JSV.pdb").read_text()
def remove_chains_and_verify... | 1,647 | 42.368421 | 91 | py |
SGA | SGA-main/setup.py | #!/usr/bin/env python
# Supports:
# - python setup.py install
#
# Does not support:
# - python setup.py test
# - python setup.py version
import os, glob
from setuptools import setup, find_packages
def _get_version():
import subprocess
version = subprocess.check_output('git describe', shell=True)
version ... | 1,244 | 20.842105 | 65 | py |
SGA | SGA-main/science/SGA2020/sga-bgspv-targets.py | #!/usr/bin/env python
import os, pdb
import numpy as np
import fitsio
from glob import glob
from astropy.table import Table, vstack, join
from desitarget.targetmask import desi_mask, bgs_mask, scnd_mask
pvnames = ['PV_BRIGHT_HIGH', 'PV_BRIGHT_MEDIUM', 'PV_BRIGHT_LOW',
'PV_DARK_HIGH', 'PV_DARK_MEDIUM', 'PV_... | 2,087 | 33.229508 | 120 | py |
SGA | SGA-main/py/SGA/galex.py | """
SGA.galex
=========
Code to generate GALEX custom coadds / mosaics.
"""
import os, pdb
import numpy as np
from astrometry.util.util import Tan
from astrometry.util.fits import fits_table
import SGA.misc
def _ra_ranges_overlap(ralo, rahi, ra1, ra2):
import numpy as np
x1 = np.cos(np.deg2rad(ralo))
y... | 13,777 | 36.237838 | 105 | py |
SGA | SGA-main/py/SGA/html.py | """
SGA.html
========
Code to generate HTML output for the various stages of the SGA analysis.
"""
import os
import numpy as np
def get_layer(onegal):
if onegal['DR'] == 'dr6':
layer = 'mzls+bass-dr6'
elif onegal['DR'] == 'dr7':
layer = 'decals-dr5'
else:
print('Unrecognized data ... | 9,966 | 33.607639 | 114 | py |
SGA | SGA-main/py/SGA/unwise.py | """
SGA.unwise
==========
Code to generate unWISE custom coadds / mosaics.
"""
import os, pdb
import numpy as np
import SGA.misc
def _unwise_to_rgb(imgs, bands=[1,2], mn=-1, mx=100, arcsinh=1.0):
"""Support routine to generate color unWISE images.
Note that the input images need to be in *Vega* nanomaggies... | 11,596 | 38.580205 | 105 | py |
SGA | SGA-main/py/SGA/qa.py | """
SGA.qa
======
Code to do produce various QA (quality assurance) plots.
"""
import os, pdb
import warnings
import time, subprocess
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import SGA.misc
#import seaborn as sns
#sns.set(style='ticks', font_scale=1.4, palette='Set2'... | 26,737 | 40.198767 | 109 | py |
SGA | SGA-main/py/SGA/io.py | """
SGA.io
======
Code to read and write the various SGA files.
"""
import os, warnings
import pickle, pdb
import numpy as np
import numpy.ma as ma
from glob import glob
import fitsio
from astropy.table import Table, Column, hstack
from astropy.io import fits
def custom_brickname(ra, dec):
brickname = '{:08d}{}... | 14,765 | 35.369458 | 133 | py |
SGA | SGA-main/py/SGA/webapp/settings.py | #!/usr/bin/env python
"""Django settings for SGA project.
Generated by 'django-admin startproject' using Django 2.0.6.
For more information on this file, see
https://docs.djangoproject.com/en/2.0/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/2.0/ref/settings/... | 3,973 | 25.317881 | 102 | py |
SGA | SGA-main/py/SGA/webapp/wsgi.py | """
WSGI config for SGA webapp project.
It exposes the WSGI callable as a module-level variable named ``application``.
For more information on this file, see
https://docs.djangoproject.com/en/2.0/howto/deployment/wsgi/
"""
import os
from django.core.wsgi import get_wsgi_application
os.environ.setdefault("DJANGO_SE... | 397 | 22.411765 | 78 | py |
SGA | SGA-main/py/SGA/webapp/load.py | #!/usr/bin/env python
"""Load the input sample into a database table.
"""
import os
import numpy as np
import fitsio
import django
from astropy.table import Table, hstack
DATADIR = '/global/cfs/cdirs/cosmo/data/sga/2020'
#DATADIR = '/global/cfs/cdirs/cosmo/work/legacysurvey/sga/2020'
def main():
from astrometr... | 2,737 | 32.390244 | 104 | py |
SGA | SGA-main/py/SGA/webapp/manage.py | #!/usr/bin/env python
"""
Used to run the server for this Django project
"""
import os, sys
if __name__ == "__main__":
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "SGA.webapp.settings")
try:
from django.core.management import execute_from_command_line
except ImportError as exc:
raise ... | 593 | 28.7 | 74 | py |
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